Structure and mechanical properties of DNA play a key role in its biological functioning. A lot of well-established conclusions about the DNA structure and its sequence-dependent variabil- ity came from various experimental and computational studies of the Dickerson-Drew dodecamer (DD), a prototypic B-DNA molecule of the sequence (5')CGCGAATTCGCG(3'). In this study we present a detailed analysis of structural and mechan- ical properties of DD based on extensive atomistic molecular dynamics (MD) simulations with explicit representation of wa- ter and ionic environment. We analyze three simulated systems covering different ionic conditions and water models. Two MD trajectories are reported for the first time, one of them being 2.4 µs long. An extensive comparsion with one recent NMR struc- ture and four recent X-ray structures is made. It is found that the end basepairs can adopt two different pairing motifs dur- ing the simulation: the canonical Watson-Crick pair or a non- canonical trans Watson-Crick/Sugar Edge pair. These states can significantly influence the structure of DD even at the third step from the end. A clear relationship is found between the BI/BII backbone substates and the basepair step conformation. A model of rigid bases is used to study mechanical properties of the DNA. The non-local...

Interaction preferences in protein - DNA complexes Dávid Jakubec Abstract Interactions of proteins with DNA lie at the basis of many fundamental bio- logical processes. Despite ongoing efforts, the rules governing the recognition of specific nucleic acid sequences have still not been universally elucidated. In this work, I attempt to explore the recognition process by splitting the intricate network of contacts at the protein - DNA interface into contribu- tions of individual amino acid - nucleotide pairs. These pairs are extracted from existing high-resolution structures of protein - DNA complexes and in- vestigated by bioinformatics and computational-chemistry based methods. Criteria of specificity based on the coupling of observed geometrical prefer- ences and the respective interaction energies are introduced. The application of these criteria is used to expand the library of amino acid - nucleotide pairs potentially significant for direct sequence recognition. Electrostatic poten- tial maps are calculated for individual nucleotides as well as for selected complexes to investigate the physical basis of the observed specificity. 1

Title: Multicomponent plasma polymers with spatially controlled properties Author: MSc. Pavel Pleskunov Department / Institute: Department of Macromolecular Physics/Charles University Supervisor of the doctoral thesis: Prof. Ing. Andrey Shukurov, PhD, Department of Macromolecular Physics / Charles University Abstract: Mixing of two (or more) polymers often leads to phase separation and to the formation of nanoscale architecture, which can be highly attractive in various applications including controllable drug delivery, fabrication of separation and solid electrolyte membranes, gas storage, etc. Different wet-chemistry techniques already exist to produce nanophase-separated polymers; however, capturing the resultant polymeric structure in a predictable manner remains a challenging task. In this thesis, a low-temperature plasma-based strategy is investigated for the production of multicomponent thin films of plasma polymers with spatially discriminated nanoscale domains. Gas aggregation cluster source is used for the fabrication of nanoparticles of plasma polymerized acrylic acid, whereas Plasma-Assisted Vapor Phase Deposition is used for the deposition of thin films of poly(ethylene oxide) plasma polymer. Embedding of nanoparticles into matrices of thermodynamically incompatible plasma polymer as well as...